bytedance / bytedance/Protenix

Constrained Condition Usage

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Dominant language
Python
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Description

I have several problems on building constraint condition from documentation.

- What's the difference between `contact` and `pocket`?
- They all have the way of assign special entity by `[entity_number, copy_index, position]`. Is the position the index of the target in special entity? Or the position should be global index?
- For `pocket`, is `binder_chain` necessary? If necessary, the reason pocket is special is that it is for protein_chain-ligand? If not necessary, then what's the difference between assign contact residues in `contact` or `pocket`?
- To achieve the best performance, should I enable `esm` or not?

Contributor guide

Open the contributing guide

Research direction

The payload names no files or tests; start by reading the documentation for constrained conditions, especially the contact, pocket, binder_chain, entity indexing, and esm questions. Done means the documentation clearly explains these distinctions, parameter semantics, and the performance trade-off around esm.

Written by the indexing model from the issue text.

Assessment

Domain
documentation
Issue type
Documentation
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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